Luciferases represent an important tool in biological studies. For example, luciferases are the preferred reporter type for use in gene reporter assays; particularly due to their high sensitivity. Indeed, this high sensitivity has led to their use as labels for antibodies and in other applications where high signal and low background are advantageous. Luciferases are also widely used to study protein:protein interactions via techniques such as protein complementation assays (PCA; as for example disclosed in WO 2008/049160); and particularly for luciferases that emit blue light, in bioluminescence resonance energy transfer (BRET).
Gene reporter assays permit an understanding of what controls the expression of a gene of interest e.g., DNA sequences, transcription factors, RNA sequences, RNA-binding proteins, signal transduction pathways and specific stimuli. In particular, reporter assays can be used to identify nucleic acid regions important in gene regulation. Such regions and/or the factors that bind or modulate them may serve as potential targets for therapeutic intervention in the treatment or prevention of human diseases. Reporter assays can also be used to screen drugs for their ability to modify gene expression.
Reporter assays can be used to identify a gene promoter region or specific elements within a promoter, such as transcription factor binding sites or other regulatory elements. Alternatively, such assays are used to study the response of a promoter or regulatory element to various stimuli or agents. In some applications, the reporter constructs used in the assay, or transfected cells, are introduced into an organism to study promoter function in vivo. Moreover, reporter assays can be used to study or measure signal transduction pathways upstream of a specific promoter. In some cases the promoter comprises a single type of transcription factor (TF) binding site, such that reporter activity reflects the activity of the pathway leading to activation of that TF.
By way of example, in the case of reporter assays designed to investigate putative promoter sequences or other transcriptional regulatory elements, nucleic acids to be interrogated are cloned into reporter plasmids in a location so as to permit the regulation of transcription of a downstream reporter gene, and thus expression of a reporter protein encoded by the reporter gene. The reporter protein should be distinguishable from endogenous proteins present in the cell in which the reporter plasmid is transfected for ease of detection, and preferably expression of the reporter protein should be readily quantifiable. The reporter protein is quantified in an appropriate assay and often expressed relative to the level of a control reporter driven by a ubiquitous promoter such as, for example, the promoter SV40. The control reporter must be distinguishable from the test reporter and is generally contained on a separate vector that is co-transfected with the test vector and used to control for transfection efficiency. Such assays are based on the premise that cells take up proportionally equal amounts of both vectors.
A variety of different applications for gene reporter assays involves measuring a change in gene expression over time or after addition of a compound, such as a drug, ligand, hormone etc. This is of particular importance in drug screening. Following the addition of the drug, detecting a measurable change in levels of the reporter protein may be delayed and diluted as changes in expression levels are transmitted through mRNA to protein. A significant advance in such applications recently made by the present applicant is the combined use of mRNA- and protein-destabilizing elements in the reporter vector to improve the speed and magnitude of response, as described in U.S. Pat. No. 7,157,272, the disclosure of which is incorporated herein by reference in its entirety.
Various reporter gene assay systems are commercially available utilizing different detectable reporter proteins, the most common being chloramphenicol transferase (CAT), β galactosidase (β-gal), secreted alkaline phosphatase, and various fluorescent proteins and luciferases.
Luciferase is the most commonly used reporter protein for in vitro assay systems. Luciferases are enzymes capable of bioluminescence and are found naturally in a range of organisms. In commercially available assay systems, luciferases can be divided into two major groups; those which utilize D-luciferin as a substrate and those which utilize coelenterazine as a substrate. The most widely employed example of the former is firefly luciferase, an intracellular enzyme. Additional examples of luciferases utilizing D-luciferin include other members of Coleoptera, such as click beetles and railroad worms. Luciferases may also be distinguished on the basis of whether the organism from which they are derived is terrestrial or aquatic (typically marine). Luciferases utilizing coelenterazine as a substrate are typically derived from marine animals such as the soft coral Renilla or copepods such as Metridia and Gaussia, whereas D-luciferin-utilizing luciferases are typically derived from terrestrial animals. A further means of distinguishing luciferases is on the basis of whether they are secreted or non-secreted in their native state; i.e., in the organism from which they are derived. Luciferases derived from terrestrial organisms are typically non-secreted (intracellular), whilst those derived from marine organisms may be secreted or non-secreted (intracellular). For example, Renilla luciferase is intracellular, whereas Gaussia luciferase in its native state is a secreted enzyme. The secretion of luciferases by marine organisms is thought to be a protective response designed to distract approaching predators. Other secreted luciferases include those from Metridia longa, Vargula hilgendorfii, Oplophorus gracilirostris, Pleuromamma xiphias, Cypridina noctiluca and other members of Metridinidae. Vargula luciferase utilizes a substrate that is different to coelenterazine or D-luciferin. Another class of luciferase is derived from dinoflagellates.
Luciferase-based assay systems may employ more than one luciferase, typically of different origin and each utilizing a different substrate, enabling both test and control reporter to be measured in the same assay. By way of example, a putative promoter element is cloned upstream of a firefly luciferase reporter gene such that it drives expression of the luciferase gene. This plasmid is transiently transfected into a cell line, along with a control plasmid containing the Renilla luciferase gene driven by the SV40 promoter. First luciferin is added to activate the firefly luciferase, activity of this reporter is measured, and then a “quench and activate” reagent is added. This “quench and activate” reagent contains a compound that quenches the luciferin signal and also contains coelenterazine to activate the Renilla luciferase, the activity of which is then measured. The level of firefly luciferase activity is dependent not only on promoter activity but also on transfection efficiency. This varies greatly, depending on the amount of DNA, the quality of the DNA preparation and the condition of the cells. The co-transfected control plasmid (Renilla luciferase driven by a suitable promoter such as the SV40 promoter) is used to correct for these variables, based on the premise that Renilla luciferase activity is proportional to the amount of firefly luciferase-encoding plasmid taken up by the cells. Alternatively or in addition, the Renilla luciferase may be used to control for other variables, such as cell number, cell viability and/or general transcriptional activity; or may be used to determine whether a particular treatment or compound applied to the cells affects both promoters or is specific to one of them.
Luciferase-based assay systems, in particular those utilizing one or more intracellular luciferases, often employ two buffers, a lysis buffer and an assay buffer. The lysis buffer is added to the cells first to lyse the cells and thus release luciferase, facilitating subsequent measurement. An assay buffer containing the luciferase substrate and any cofactors is then added, after which measurement of luciferase activity is taken. Measurement may be made immediately (i.e., within seconds) of the addition of the assay buffer (so-called “flash” reaction), or minutes or hours later (so-called “glow” reactions) by using “glow” reagents in the assay buffer that keep the light signal stable for an extended period of time. Flash reactions provide the highest signal strength (light units per second) and thereby have the advantage of providing the highest sensitivity. Glow reactions are particularly advantageous in applications where, for example, the user does not have a suitable luminometer (equipped with injectors) readily available or in some high throughput screening applications where batch-processing requires a delay between injection and measurement.
Secreted luciferases are measured in samples of the conditioned medium surrounding the test cells. As such, lysis buffers are typically not used with secreted luciferases. Secreted luciferases from copepods such as Metridia and Gaussia species are not only the smallest known luciferases but also provide the highest sensitivity of all known luciferases. Both of these features are clearly advantageous but the latter feature is of particular importance where the reporter gene assayed provides only low levels of luciferase in the cells of interest, for example, where the promoter being studied has only low activity, and/or where the cells of interest are difficult to transfect/transduce with the reporter vector. A further increase in sensitivity would also facilitate the miniaturization of reporter assays by reducing the minimum number of cells required to yield a signal strength that can be reliably measured.
When utilizing assay systems including destabilizing elements such as those described in U.S. Pat. No. 7,157,272, the steady-state luciferase signal is reduced. Thus luciferases that provide higher signal strength would be particularly advantageous for reporter assay systems utilizing destabilizing elements.
As stated above, the luciferases that provide the highest sensitivity are secreted luciferases from the family of luciferases that include copepods such as Metridia and Gaussia (also referred to herein as “copepod luciferases,” “copepod family of luciferases” and the like). However, in some applications it is preferable to use non-secreted luciferases. For example, to enable the use of protein destabilizing elements and thereby improve responsiveness. Consequently, non-secreted versions of copepod luciferases have been developed; for example by removing the functional signal peptide, as disclosed for instance in WO 2008/049160.
A common feature of this family of luciferases is their dependence on folding via the formation of disulfide bridges between their ten conserved cysteines, often designated C1 to C10. This feature was recently utilized to develop novel multi-luciferase assays that employ a reducing agent such as DTT to switch off the luciferase or shorten its period of light emission, thereby enabling measurement of a different luciferase in the same sample, as disclosed for example in WO 2008/074100.
In other applications, there is currently a compromise between “flash” and “glow” buffers and luciferases. That is, to obtain an intense flash, the glow phase is sacrificed and vice versa. There is a clear need for systems that can provide a high sensitivity flash reaction but also provide a prolonged glow. Luciferases facilitating the generation of both high flash and prolonged glow from luciferase-catalyzed bioluminescence reactions would provide the user with a dual purpose reagent that can provide high sensitivity (flash reactions) where needed but also provide the convenience of glow reactions for applications where high sensitivity is not required.
To improve the accuracy of luciferase-based assays it is desirable to minimize the effect of unwanted or unavoidable variables on the activity of the luciferase. One such variable is temperature. Most in vitro luciferase-based assays are performed on a laboratory bench at “room temperature”. However, it is often impractical or impossible to provide a constant temperature within the samples. For example, the measuring device (e.g. luminometer) typically generates heat, which raises the reaction temperature over time during measurement. This creates inaccuracy because, for example, the reaction temperature is higher in the last sample measured than in the first sample measured; and the measured parameter (luminescence) is affected by temperature as well as by the amount of luciferase present in the sample.
Additionally, the samples and assay reagents are often stored in a fridge or freezer prior to measurement; and variations in the extent of warming prior to initiation of the reaction are not uncommon in practice. Clearly, it is desirable to have a luciferase that displays minimal change in activity in response to fluctuations in temperature above and below room temperature. A particularly desirable feature would be minimal change in activity in response to temperature rises above room temperature, which occur within luminometers.
Additionally, it is desirable to hive a luciferase with an optimal temperature at or about the intended temperature of the measurement assay. For example, this would provide greater sensitivity. As indicated above, room temperature is common for many in vitro luciferase assays. However, 37° C. would be preferable for certain in vivo assays, such as those performed within a living mammal. Other luciferase assays (e.g., as an antibody label) would preferably be performed at or about 4° C. in order to minimize degradation of essential reaction components in the sample and/or assay reagent.
Accordingly, it would be advantageous to be able to customize a luciferase by adjusting its optimal temperature and temperature effect according to the preferred parameters of the intended assay type.
There are a number of disadvantages associated with the known copepod luciferases from Metridia and Gaussia. In particular, there is a need for luciferases that provide improved sensitivity and accuracy in luciferase reactions. For example, a flash signal strength of greater intensity than is achievable with existing luciferases; and/or a glow signal that is either of greater intensity and/or more stable over time; and/or a temperature effect that is more suitable for the intended assay type.
It would be particularly advantageous to determine the type of structural changes or elements in these luciferases that convey the desirable features. Such knowledge would enable customization and optimization of luciferases, including luciferases within the copepod luciferase family.